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Changes to the GEP Web Framework - Fall 2012

Posted: Sat Aug 25, 2012 5:52 pm
by wleung
Hello Everyone,

The Project Management System has been reset for Fall 2012. A new set of 70 projects derived from the Muller F element of D. biarmipes is now available to be claimed on the Project Management System. You can view the projects using the GEP UCSC Genome Browser Mirror by selecting “D. biarmipes” under the “genome” field on the Genome Gateway page. The D. biarmipes projects have RNA-Seq data from three libraries: adult males, adult females and mixed embryos. The Genome Browser contains evidence tracks for the alignment coverage summary, TopHat, Cufflinks, and Oases transcripts tracks for each of these libraries. The new genome also contains conservation tracks based on sequence alignments against the whole genome assemblies of seven species closely related to D. biarmipes.

Because the D. biarmipes whole genome assembly has not been manually improved, the assembly might contain errors in the consensus that would lead to frame-shifts or in-frame stop codons in the gene models. We have developed techniques to extract and assemble a region of the 454 whole genome assembly and examine the assembly using Consed. Please contact either Chris or me if you suspect there is an error in the consensus sequence.

Based on the efforts of the GEP faculty members during the August alumni workshop, we have revised the GEP Annotation Report. In addition to clarifying the report requirements, the new report form requires an additional screenshot from the Annotation Files Merger that shows all the annotated gene models on the Genome Browser. You can find the user guide for the Annotation Files Merger under "Help" -> "Documentations" -> "Web Framework." The new report form has been incorporated into all of the annotation packages. You can download the new GEP Annotation Report form through the GEP web site.

All the annotation resources have been updated to FlyBase release 5.46. Because some of GEP faculty members are using the projects from D. erecta, D. mojavensis and D. grimshawi for teaching purposes, I have updated the packages and blastx alignment tracks for all of the projects from these species even though they are no longer available for claiming in the production Project Management System. Note that you can still claim these projects using the demo Project Management System.

We have also made many improvements to the GEP web framework. The key changes are listed below:

1. GEP UCSC Genome Browser Mirror
- Upgrade Genome Browser to release 270
(New navigation features: right click context menu, pan and zoom)
- mRNA alignment track from SPALN2
- Improved D. melanogaster protein alignment tracks and ortholog predictions (genBlastG and D. mel Chained Proteins)
- Multiz, chain, net alignments of 7 species closely related to D. biarmipes
(Identify highly conserved regions with PhastCons)

2. Synchronize annotation resources to FlyBase release 5.46
- Annotation packages
- BLASTX alignment tracks on the GEP Genome Browser Mirror
- Annotation Files Merger
- Gene Record Finder
- Gene Model Checker

3. Annotation Files Merger
- Improved isoform checklist for checking gene names and number of isoforms
- Detect features with overlapping coordinates
- Added separate user guide on how to use the Annotation Files Merger to identify common submission errors
- Added drag and drop functionality for modern browsers

4. GEP Project Management System
- Update web interface to maintain compatibility with newer web browsers
- Detect large annotation report files
- Improve detection of corrupted file uploads

5. Updates to curriculum materials
We have updated the following curriculum materials to maintain compatibility with current versions (as of 08/16/2012) of NCBI, FlyBase, ExPASy, and the Gene Record Finder. Many of these changes are caused by the fact that NCBI has added compositional adjustments to blastx searches by default.

- A Simple Introduction to NCBI BLAST
- Introduction to ab initio and Evidence-based Gene Finding
- Simple Annotation Problem
- Exercise #1: Detecting and Interpreting Genetic Homology
- Chimp BAC Analysis
- Annotation for D. virilis
- GEP Annotation Report
- Annotation Strategy Guide
- Primer on Reading Frames and Phase
- Common Annotation Errors

Please let me know if you have any questions or concerns. Thanks.